There isnt any way for the program to slow down hard ware
The repairs are 95% registry related. When you say slowed down, what exactly do you mean? By how much? Do you have any speed tests to show before and after? What version of Windows? What repairs where ran? What tweaks where done?
I need some info to go on and I can help you look into it and find out what is going on.
The only way there would be a drive speed difference after the repairs would be from the Windows services that are put back to their default startups, such as Windows Search, it catalogs all the files on the drive and so reads and writes to the drive. So the more things using the drive the slower it will be.
Shane